Molecular metrics status: done
Cached molecular metrics are available for this pose.
Metrics cached · SASA missing
py3Dmol interaction viewer
Left: interactive complex viewer. Right: clickable PLIP-like interaction summary. Clicking an interaction thickens and highlights it in the 3D view.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.399 kcal/mol/HA)
✓ Good fit quality (FQ -13.63)
✓ Strong H-bond network (15 bonds)
✗ Very high strain energy (29.5 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-43.358
kcal/mol
LE
-1.399
kcal/mol/HA
Fit Quality
-13.63
FQ (Leeson)
HAC
31
heavy atoms
MW
449
Da
LogP
1.75
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 29.5 kcal/mol
Interaction summary
Collapsible panels
H-bonds 15
Hydrophobic 24
π–π 3
Clashes 17
Severe clashes 1
| Final rank | 9.9085794574414 | Score | -43.3583 |
|---|---|---|---|
| Inter norm | -1.40297 | Intra norm | 0.00431988 |
| Top1000 | no | Excluded | yes |
| Contacts | 18 | H-bonds | 15 |
| Artifact reason | excluded; geometry warning; 10 clashes; 1 protein clash; high strain Δ 52.1 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:LEU208;A:LEU209;A:LYS178;A:LYS220;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER207;A:SER95;A:TRP221;A:TYR174;A:VAL206 | ||
Protein summary
275 residues
| Protein target | T07 | Atoms | 3932 |
|---|---|---|---|
| Residues | 275 | Chains | 3 |
| Residue summary | LEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | TbPTR1_cW_6RX6_Ready | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 6 |
| IFP residues | A:ARG14; A:ASP161; A:CYS168; A:GLY205; A:LEU208; A:LEU209; A:LYS178; A:MET213; A:NAP301; A:PHE171; A:PHE97; A:PRO210; A:PRO99; A:SER207; A:SER95; A:TRP221; A:TYR174; A:TYR98; A:VAL206 | ||
| Current overlap | 16 | Native recall | 0.84 |
| Jaccard | 0.76 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.67 |
| H-bond same residue+role | 3 | Role recall | 0.60 |
| H-bond same residue | 3 | Residue recall | 0.60 |
Hydrogen bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
Hydrophobic contacts
Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | Contacts | Native overlap | Native recall | HB role recall | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2583 | 4.2209894816256535 | -0.555313 | -16.1207 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2515 | 4.652823965092423 | -0.727316 | -22.3899 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 3722 | 4.960094695259888 | -0.668832 | -18.5156 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2328 | 5.5951612106632655 | -0.851481 | -22.659 | 8 | 18 | 16 | 0.84 | 0.40 | - | no | Open |
| 2511 | 5.862969908742773 | -0.779095 | -23.3679 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 2590 | 5.890746353274221 | -0.612518 | -17.7237 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 3725 | 6.7517751962758155 | -0.680338 | -17.0115 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2732 | 7.304912037411356 | -0.645105 | -19.1975 | 9 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 2969 | 7.316665648863985 | -0.88242 | -25.3901 | 12 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2586 | 5.3922107497825715 | -0.585657 | -15.232 | 6 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2327 | 5.73597683987735 | -1.11724 | -33.1273 | 8 | 19 | 19 | 1.00 | 0.60 | - | yes | Open |
| 2509 | 6.439355314132002 | -0.798632 | -23.4584 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2733 | 6.738774018392601 | -0.620425 | -18.8691 | 8 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2975 | 6.8049506376120945 | -0.813956 | -26.1024 | 13 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3718 | 6.898755068777284 | -0.688191 | -21.5251 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2973 | 7.128940867640139 | -0.929142 | -28.3549 | 14 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2518 | 7.246102087887385 | -0.85957 | -24.6584 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2977 | 7.286076590115401 | -0.902553 | -32.9808 | 16 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2585 | 7.325731875266721 | -0.63896 | -16.3253 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2588 | 7.518112891610314 | -0.63591 | -18.8044 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2582 | 7.658523251084196 | -0.622288 | -18.018 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3727 | 7.671885605455082 | -0.747246 | -19.5367 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2730 | 7.683699295111764 | -0.844102 | -23.969 | 8 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2581 | 7.753640291670464 | -0.641628 | -17.3082 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2974 | 7.832893107937096 | -0.590531 | -14.4477 | 12 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2727 | 7.883690695340405 | -0.87096 | -22.8257 | 9 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2735 | 8.023397663060127 | -0.780416 | -20.3292 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2517 | 8.127766704637024 | -0.885413 | -25.7361 | 7 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2726 | 8.154017001741906 | -0.832495 | -19.6828 | 12 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2329 | 8.178156362938102 | -0.941753 | -27.0028 | 11 | 18 | 14 | 0.74 | 0.60 | - | yes | Open |
| 2510 | 8.262448841504611 | -0.870826 | -23.738 | 9 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2589 | 8.315516089699077 | -0.660327 | -18.0549 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2333 | 8.42926478489393 | -1.01858 | -28.1393 | 11 | 16 | 12 | 0.63 | 0.60 | - | yes | Open |
| 2513 | 8.550208654850088 | -0.928268 | -27.106 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3719 | 8.727873827452708 | -0.819792 | -23.1151 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2514 | 8.792040911108568 | -0.818419 | -26.1901 | 9 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2729 | 9.057675263325125 | -0.799314 | -18.3904 | 13 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2728 | 9.283331156834386 | -0.7675 | -23.5429 | 13 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2587 | 9.285854373675479 | -0.699326 | -17.7051 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2584 | 9.29710076816024 | -0.62264 | -18.3999 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3720 | 9.34343170031126 | -0.767049 | -24.1366 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2516 | 9.570291170471489 | -0.725497 | -22.3814 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2972 | 9.61940344050051 | -0.715755 | -19.5906 | 10 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2734 | 9.759229743270597 | -0.830676 | -21.8977 | 9 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3724 | 9.791473931831877 | -0.753623 | -16.2935 | 9 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2335 | 9.9085794574414 | -1.40297 | -43.3583 | 15 | 18 | 16 | 0.84 | 0.60 | - | yes | Current |
| 2331 | 10.88824850472598 | -1.12896 | -30.7873 | 10 | 18 | 15 | 0.79 | 0.40 | - | yes | Open |
| 2512 | 11.044204631278706 | -0.831552 | -23.1002 | 10 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2971 | 11.385762776942663 | -0.720755 | -18.5838 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2978 | 12.155236657325428 | -0.748444 | -19.8444 | 10 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3721 | 12.390850300677714 | -0.773653 | -22.8479 | 7 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3723 | 12.48523049266267 | -0.761753 | -21.2363 | 12 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2334 | 12.638027492794226 | -0.979413 | -26.0569 | 12 | 19 | 17 | 0.89 | 0.60 | - | yes | Open |
| 2330 | 12.77774780376639 | -0.862745 | -22.4608 | 10 | 19 | 16 | 0.84 | 0.60 | - | yes | Open |
| 2326 | 13.063895391318354 | -0.973377 | -19.8963 | 9 | 20 | 16 | 0.84 | 0.60 | - | yes | Open |
| 3726 | 13.418619973292195 | -0.681677 | -12.1469 | 9 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2731 | 13.883270037725907 | -0.620857 | -18.4987 | 14 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2976 | 14.439532037555631 | -0.811317 | -22.1788 | 14 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2332 | 15.974165041283914 | -0.810722 | -18.2268 | 14 | 20 | 16 | 0.84 | 0.60 | - | yes | Open |
| 2970 | 19.413207846850757 | -0.813274 | -22.0289 | 15 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-43.358kcal/mol
Ligand efficiency (LE)
-1.3987kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.626
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
449.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.75
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.51kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
64.67kcal/mol
Minimised FF energy
35.15kcal/mol
SASA & burial (FreeSASA)
not yet run
SASA has not been computed yet for this pose. Queue a background recompute to populate FreeSASA burial metrics without blocking the page.